By using microreactors fabricated with silicon microtechnology, heterogeneous catalyzed gas-phase reactions can be studied which are difficult to control because of their exothermic nature, are explosive or use toxic/hazardous gases. In this type of microreactors, catalytic materials like rhodium or platinum are deposited on a thin membrane in deep trenches. Conventional techniques, like lift-off lithography, cannot be used in deep trenches and deposition through flat shadow masks does not yield well-defined regions of catalyst. For well-controlled deposition of a catalytic thin film on a membrane located in a deep trench, a technique is developed using sputter deposition with a 3-dimensionally shaped 'self-aligning' shadow mask.